In an unusual move for the company, Nintendo decided to start work on a sequel right away, using the same engine as Ocarina of Time. After investing four years of development time, Nintendo wanted to re-use some of those resources with a new game, initially planned as a "gaiden" title (a side story, not part of the "main" series). Miyamoto was less involved with the project this time, leaving his protégée Eiji Aonuma in charge of the team. While ostensibly very similar to Link's last adventure, Aonuma doesn't like treading the same path, so there were some major changes thrown into the reused framework.

A true sequel (or mid-quel, since the time travel aspect makes that label complicated), it followed young Link after the close of his adventures in Ocarina of Time. He discovers a plot to destroy the world by plunging the moon into the face of the planet. The story takes some darker, even genuinely sad turns along the way, as Link fights against time to save the world again. It's only by virtue of his trusty Ocarina that he is able to complete his quest in time at all.

The game was locked to a three-day time cycle that could be repeated at will, trapping Link in an endless cycle of real-time progression, like a fantasy version of the film Groundhog's Day. This unusual structure was not the only change, however. The game also introduced masks which allowed Link to transform into other races. The shift in design drew its fair share of criticism, but at least it dodged accusations of rehashing. Even with the same fundamental mechanics, Majora's Mask was a very different experience.

Majora's Mask brought a close to the Nintendo 64 era, and sold a somewhat more modest three million copies when all was said and done. That might have as much to do with the waning interest in the Nintendo 64 as it did with anyone's disappointment in the game, but it still marked a commercial low point for the series. Luckily, Nintendo did not decide to take time off for another five years.

With the success of the colorized Link's Awakening DX, Nintendo was hoping to see some original Zelda action on their newly revitalized 8-bit handheld. Miyamoto was occupied with more important things, so Nintendo decided to outsource, leaving the project in the capable hands of Capcom's Yoshiki Okamoto, and his team at Flagship.

Okamoto was a long time fan, not to mention one of the giants of the industry, but that doesn't mean that development didn't have its fare share of problems. Initially, he waffled between remaking the first Zelda and starting an original project, before eventually settling on a trilogy of companion games that could all interact with each other.

The innovative system proved to be too complicated, and the constant changes to the scenario pushed the release back further and further. Eventually he decided to scrap the trilogy plan and focus on just two games: Oracle of Ages and Oracle of Seasons.

Despite the long development time, the two games recycled most of their graphics from Link's Awakening, and the gameplay remained very faithful to Link's first handheld outing. Even still, the scenarios for each were ambitious. Oracle of Ages relied on a time travel premise, while Seasons had time-sensitive puzzles based on the changing of the seasons.

Unlike the CD-i games, the two Oracle games were able to actually interact with each other with more than just passing references. After completing one game, you'd be given a password that allowed your actions to affect the world of the second game. Earlier in their cycle, some shrugged off the twin-game release as another attempt to cash in on the fad begun by Pokemon, but in practice it was a novel enhancement to encourage fans to experience both games, which were quite different in their own right.